🔖 9th International Conference on Complex Systems | NECSI

9th International Conference on Complex Systems | NECSI (necsi.edu)
The International Conference on Complex Systems is a unique interdisciplinary forum that unifies and bridges the traditional domains of science and a multitude of real world systems. Participants will contribute and be exposed to mind expanding concepts and methods from across the diverse field of complex systems science. The conference will be held July 22-27, 2018, in Cambridge, MA, USA. Special Topic - Artificial Intelligence: This year’s conference will include a day on AI, including its development and potential future. This session will be chaired by Iyad Rahwan of MIT's Media Lab.

A great looking conference coming up with a strong line up of people who’s work I appreciate. It could certainly use some more balance however as it’s almost all white men.

In particular I’d want to see:
Albert-László Barabási (Northeastern University, USA)
Nassim Nicholas Taleb (Real World Risk Institute, USA)
Stuart Kauffman (Institute for Systems Biology, USA)
Simon DeDeo (Carnegie Mellon University, USA)
Stephen Wolfram (Wolfram Research)
César Hidalgo (MIT Media Lab, USA)

Others include:
Marta González (University of California Berkeley, USA)
Peter Turchin (University of Connecticut, USA)
Mercedes Pascual (University of Chicago, USA) Pending confirmation
Iyad Rahwan (MIT Media Lab, USA)
Sandy Pentland (MIT Media Lab, USA)
Theresa Whelan (U.S. Department of Defense) Pending DOD approval
H. Eugene Stanley (Boston University, USA)
Ricardo Hausmann (Harvard University, USA)
Stephen Grossberg (Boston University, USA)
Daniela Rus (MIT Computer Science & Artificial Intelligence Lab, USA) Pending confirmation
Olaf Sporns (Indiana University Network Science Institute, USA)
Michelle Girvan (University of Maryland, USA) Pending confirmation
Cameron Kerry (MIT Media Lab, USA)
Irving Epstein (Brandeis University, USA)

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🔖 [1801.06022] Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors | arXiv

Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors by Yonatan Yehezkeally and Moshe Schwartz (arxiv.org)
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction problem, which is applicable whenever multiple reads of noisy data are available. This strategy is uniquely suited to the medium, which inherently replicates stored data in multiple distinct ways, caused by mutations. We consider noise introduced solely by uniform tandem-duplication, and utilize the relation to constant-weight integer codes in the Manhattan metric. By bounding the intersection of the cross-polytope with hyperplanes, we prove the existence of reconstruction codes with greater capacity than known error-correcting codes, which we can determine analytically for any set of parameters.
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📖 Read pages 19-52 of The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📖 Read Chapter 1: What is Life? pages 19-52 in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane (W.W. Norton,
, ISBN: 978-0393088816)

Lane lays out a “brief” history of the 4 billion years of life on Earth. Discusses isotopic fractionation and other evidence that essentially shows a bottleneck between bacteria and archaea (procaryotes) on the one hand and eucaryotes on the other, the latter of which all must have had a single common ancestor based on the genetic profiles we currently see. He suggest that while we should see even more diversity of complex life, we do not, and he hints at the end of the chapter that the reason is energy.

In general, it’s much easier to follow than I anticipated it might be. His writing style is lucid and fluid and he has some lovely prose not often seen in books of this sort. It’s quite a pleasure to read. Additionally he’s doing a very solid job of building an argument in small steps.

I’m watching closely how he’s repeatedly using the word information in his descriptions, and it seems to be a much more universal and colloquial version than the more technical version, but something interesting may come out of it from my philosophical leanings. I can’t wait to get further into the book to see how things develop.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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📗 Started reading The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📗 Started reading pages 1-18 Introduction: Why is Life the Way it is in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

A quick, but interesting peek into where he intends to go. He lays out some quick background here in the opening. He’s generally a very lucid writer so far. Can’t wait to get in further.

Some may feel like some of the terminology is a hurdle in the opening, so I hope he circles around to define some of his terms a bit better for the audience I suspect he’s trying to reach.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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Energy and Matter at the Origins of Life by Nick Lane | Santa Fe Institute

Energy and Matter at the Origin of Life by Nick Lane (Santa Fe Institute Community Event (YouTube))
All living things are made of cells, and all cells are powered by electrochemical charges across thin lipid membranes — the ‘proton motive force.’ We know how these electrical charges are generated by protein machines at virtually atomic resolution, but we know very little about how membrane bioenergetics first arose. By tracking back cellular evolution to the last universal common ancestor and beyond, scientist Nick Lane argues that geologically sustained electrochemical charges across semiconducting barriers were central to both energy flow and the formation of new organic matter — growth — at the very origin of life. Dr. Lane is a professor of evolutionary biochemistry in the Department of Genetics, Evolution and Environment at University College London. His research focuses on how energy flow constrains evolution from the origin of life to the traits of complex multicellular organisms. He is a co-director of the new Centre for Life’s Origins and Evolution (CLOE) at UCL, and author of four celebrated books on life’s origins and evolution. His work has been recognized by the Biochemical Society Award in 2015 and the Royal Society Michael Faraday Prize in 2016.

h/t Santa Fe Institute

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The Chemical Basis of Morphogenesis by Alan Turing

a tweet by Michael Nielsen (Twitter)

Looks like Alan Turing, like Claude Shannon, was interested in microbiology too! I’ll have to dig into this. [pdf]

🔖 Upcoming Special Issue “Information Theory in Neuroscience” | Entropy (MDPI)

Special Issue "Information Theory in Neuroscience" (Entropy | MDPI)
As the ultimate information processing device, the brain naturally lends itself to be studied with information theory. Application of information theory to neuroscience has spurred the development of principled theories of brain function, has led to advances in the study of consciousness, and to the development of analytical techniques to crack the neural code, that is to unveil the language used by neurons to encode and process information. In particular, advances in experimental techniques enabling precise recording and manipulation of neural activity on a large scale now enable for the first time the precise formulation and the quantitative test of hypotheses about how the brain encodes and transmits across areas the information used for specific functions. This Special Issue emphasizes contributions on novel approaches in neuroscience using information theory, and on the development of new information theoretic results inspired by problems in neuroscience. Research work at the interface of neuroscience, Information Theory and other disciplines is also welcome. A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Information Theory". Deadline for manuscript submissions: 1 December 2017
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👓 EXCLUSIVE: First human embryos edited in U.S., using CRISPR | MIT Technology Review

EXCLUSIVE: First human embryos edited in U.S., using CRISPR by Steve Connor (MIT Technology Review)
Researchers have demonstrated they can efficiently improve the DNA of human embryos.
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👓 First Support for a Physics Theory of Life | Quanta Magazine

First Support for a Physics Theory of Life by Natalie Wolchover (Quanta Magazine)
Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

Interesting article with some great references I’ll need to delve into and read.

The situation changed in the late 1990s, when the physicists Gavin Crooks and Chris Jarzynski derived “fluctuation theorems” that can be used to quantify how much more often certain physical processes happen than reverse processes. These theorems allow researchers to study how systems evolve — even far from equilibrium.

I want to take a look at these papers as well as several about which the article is directly about.

Any claims that it has to do with biology or the origins of life, he added, are “pure and shameless speculations.”

Some truly harsh words from his former supervisor? Wow!

maybe there’s more that you can get for free

Most of what’s here in this article (and likely in the underlying papers) sounds to me to have been heavily influenced by the writings of W. Loewenstein and S. Kauffman. They’ve laid out some models/ideas that need more rigorous testing and work, and this seems like a reasonable start to the process. The “get for free” phrase itself is very S. Kauffman in my mind. I’m curious how many times it appears in his work?

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📺 A Universal Theory of Life: Math, Art & Information by Sara Walker

A Universal Theory of Life: Math, Art & Information from TEDxASU
Dr. Walker introduces the concept of information, then proposes that information may be a necessity for biological complexity in this thought-provoking talk on the origins of life. Sara is a theoretical physicist and astrobiologist, researching the origins and nature of life. She is particularly interested in addressing the question of whether or not “other laws of physics” might govern life, as first posed by Erwin Schrodinger in his famous book What is life?. She is currently an Assistant Professor in the School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science at Arizona State University. She is also Fellow of the ASU -Santa Fe Institute Center for Biosocial Complex Systems, Founder of the astrobiology-themed social website SAGANet.org, and is a member of the Board of Directors of Blue Marble Space. She is active in public engagement in science, with recent appearances on “Through the Wormhole” and NPR’s Science Friday.

Admittedly, she only had a few short minutes, but it would have been nice if she’d started out with a precise definition of information. I suspect the majority of her audience didn’t know the definition with which she’s working and it would have helped focus the talk.

Her description of Speigelman’s Monster was relatively interesting and not very often seen in much of the literature that covers these areas.

I wouldn’t rate this very highly as a TED Talk as it wasn’t as condensed and simplistic as most, nor was it as hyper-focused, but then again condensing this area into 11 minutes is far from simple task. I do love that she’s excited enough about the topic that she almost sounds a little out of breath towards the end.

There’s an excellent Eddington quote I’ve mentioned before that would have been apropos to have opened up her presentation that might have brought things into higher relief given her talk title:

Suppose that we were asked to arrange the following in two categories–

distance, mass, electric force, entropy, beauty, melody.

I think there are the strongest grounds for placing entropy alongside beauty and melody and not with the first three.

Sir Arthur Stanley Eddington, OM, FRS (1882-1944), a British astronomer, physicist, and mathematician
in The Nature of the Physical World, 1927


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🔖 The hidden simplicity of biology by Paul C W Davies and Sara Imari Walker | Reports on Progress in Physics

The hidden simplicity of biology (Reports on Progress in Physics)
Life is so remarkable, and so unlike any other physical system, that it is tempting to attribute special factors to it. Physics is founded on the assumption that universal laws and principles underlie all natural phenomena, but is it far from clear that there are 'laws of life' with serious descriptive or predictive power analogous to the laws of physics. Nor is there (yet) a 'theoretical biology' in the same sense as theoretical physics. Part of the obstacle in developing a universal theory of biological organization concerns the daunting complexity of living organisms. However, many attempts have been made to glimpse simplicity lurking within this complexity, and to capture this simplicity mathematically. In this paper we review a promising new line of inquiry to bring coherence and order to the realm of biology by focusing on 'information' as a unifying concept.

Downloadable free copy available on ResearchGate.

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🔖 The “Hard Problem” of Life by Sara Imari Walker & Paul C.W. Davies

The "Hard Problem" of Life (arXiv)
Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard - that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles. Comments: To appear in "From Matter to Life: Information and Causality". S.I. Walker, P.C.W. Davies and G.F.R. Ellis (eds). Cambridge University Press
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🔖 The Algorithmic Origins of Life – Sara Walker (SETI Talks)

The Algorithmic Origins of Life by Sara I. Walker (SETI Institute Talks)
The origin of life is arguably one of the greatest unanswered questions in science. A primary challenge is that without a proper definition for life -- a notoriously challenging problem in its own right -- the problem of how life began is not well posed. Here we propose that the transition from non-life to life may correspond to a fundamental shift in causal structure, where information gains direct, and context-dependent, causal efficacy over matter, a transition that may be mapped to a nontrivial distinction in how living systems process information. Dr. Walker will discuss potential measures of such a transition, which may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.
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